Genes, genomes & transposable elements contribution to plant-microbe interaction: a sugarcane study case

Abstract

Plant-Microbe interaction is a fundamental process in the biosphere that impacts natural ecosystems as well as agroecosystems. The understanding of the biological components and processes that control this interaction is expected to improve crop productivity and monitor environmental quality. Our approach to tackle this complex system is to use genome-wide molecular and bioinformatic tools to uncover key genes that control and/or mediate the interaction of sugarcane with three pathogens (Leifsonia xyli subsp. xyli; Xanthomonas albilineans; Sporisorium scitamineum) and a nitrogen fixing bacteria (Gluconacetobacter) considered to be beneficial to sugarcane. Those organisms have a biotrophic interaction with sugarcane and the molecular aspects under biotrophy/hemibiotrophic are generally less understood. We aim to compare and contrast molecular responses across the individual interactions on both the host and on the microorganisms. Specifically, we will (i) focus on the expression patterns of a previously identified collection of resistance gene analogs (RGA) of sugarcane as well as of genes of specific metabolic responses involved in microbe interactions such as reactive oxygen species (ROS), carbohydrate metabolism, hormone synthesis and regulation, transposable elements genes, and a gene family related to gene editing in organelles and known to have members that are involved in the regulation of plant defenses via Nat- siRNA (pentatricopeptide); (ii) evaluate and compare across species the expression patterns of microbial genes with a particular focus on their secreted molecules among which one is expected to find effectors ; (iii) evaluate and compare changes in the expression patterns during two mixed infections, and (iv) evaluate and compare changes in the microbiome of the host as a result of the interaction with the mentioned microbes. As outreach products, we expect to deliver molecular information on the biology of sugarcane when interacting with various microbes looking forward to the development of a diagnostic kit to monitor sugarcane fields and to build a comprehensive sugarcane phytobiome database that could be used in comparative studies with other Poaceae. (AU)